Hmm.  Well, simply put, it would be a massive project.  The sheer scale of it would make it utterly different to everything Pokémon has done before, as well as extremely difficult, and would necessitate throwing out a lot of the established gameplay and storyline conventions.  As cool as it would be, I think that such a mammoth project would be impractical for a cartridge game, and that the details would suffer as the designers attempted to cram everything in.  Now, for something like an MMORPG, it might be more practical, but to my knowledge Game Freak have never expressed any interest in MMO Pokémon (besides, I just plain don’t like MMORPGs).  Maybe for a strategy game it could work?  But no, for a traditional Pokémon game, I just don’t see it happening, and I think the attempt would likely be ruinous.

Stats first: Well, I’ve always assumed that a ‘Jolly’ nature meant jolly by the standards of that species.  A ‘Quiet’ Ludicolo, for instance, is noticeably less outrageous and excitable than the average Ludicolo, but still much louder and crazier than, say, a Jolly Yamask (basically a Yamask who occasionally manages to display a certain black sense of humour about being trapped in a perpetual living hell on the wrong side of the great beyond).  You might actually be able to use this to perform a rudimentary psychological comparison of two closely related types of Pokémon – Nidoking and Nidoqueen, for instance, are physically very similar, so Nidoking’s higher offensive stats and lower defensive stats might indicate a universal predisposition towards personality traits like loneliness, rashness, hastiness, and so on (which, of course, would tie in nicely with my ‘theory’ of Pokémon gender – link for new readers).

And stones: The exact physiological mechanism is quite beyond me, I’m afraid, but I did make a suggestion in this post that attempts to explain why some Pokémon use stones to evolve.  The conjecture, in brief, is that the forms triggered by the stones used to be natural evolutions of the Pokémon that have them, but have become vestigial because they’re no longer suited to changing environmental conditions – maybe achieving those forms has become too energy-intensive to be practical, or the species has come to benefit more from small size and agility than from power or intelligence.  They still have all the genes that code for the evolved form itself, but they no longer possess the regulatory genes that actually trigger the evolution, which now requires some outside stimulus (again, I unfortunately have no idea what exactly this stimulus is or how the stones provide it).  I imagine the split evolution patterns of Snorunt and Kirlia indicate something similar: those species used to evolve differently depending on gender (so, millions of years ago, all masculine Kirlia became Gallade and all feminine Snorunt became Froslass, without the need for a Dawn Stone) but, for whatever reason, Gallade and Froslass became unnecessary to the survival of the species, so that male Gardevoir and female Glalie gradually replaced the alternate forms.  This is, incidentally, a much easier account to imagine if you accept my belief that Pokémon don’t have biologically differentiated sexes, since there’s no need to explain how on earth Gardevoir started to develop male reproductive organs – in theory, a ‘masculine’ Gardevoir could always have existed and would have been able to reproduce normally, but they would originally have been weird anomalies, whereas now they’re perfectly ordinary.